Molecular dynamics investigations on the effect of D amino acid substitution in a triple-helix structure and the stability of collagen

Journal of Physical Chemistry B

Volumn 113, Issue 26, 2009, Pages 8983-8992

  Punitha, V ^a   Raman, S Sundar ^a   Parthasarathi, R ^a   Subramanian, V ^a   Rao, J Raghava ^a   Nair, Balachandran Unni ^a   Ramasamr, T ^b  

^a CENTRAL LEATHER RESEARCH INSTITUTE   (India)

^b DEPARTMENT OF SCIENCE AND TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

AMINATION; AMINO ACIDS; BIOCHEMICAL ENGINEERING; COLLAGEN; DYNAMICS; GENETIC ENGINEERING; MOLECULAR DYNAMICS; ORGANIC ACIDS; PEPTIDES; STABILITY;

AMBER FORCE-FIELD; BIOLOGICAL ACTIVITIES; COLLAGEN-LIKE PEPTIDES; D-AMINO ACID; DESTABILIZATION ENERGY; GENETIC DISORDERS; HELIX STRUCTURES; HELIX-HELIX INTERACTIONS; L-AMINO ACIDS; LOCAL PERTURBATION; MOLECULAR DYNAMICS METHODS; OSTEOGENESIS IMPERFECTA; PROTEIN ENGINEERING; RELATIVE ORIENTATION; STRUCTURAL STABILITIES; TRIPLE HELICAL STRUCTURES;

AMINES;

EID: 67649500001     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp808690m     Document Type: Article

References (85)

1. Lehninger, A. L.; Nelson, D. L.; Cox, M. M. Principles of Biochemistry, 2nd ed.; CBS Publications, Worth Publishers: New York, 1993; p 114.
2. Bonner, W. A. Chirality 2000, 12, 114.
3. Gineyts, E.; Cloos, P. A. C.; Borel, O.; Grimaud, L.; Delmas, P. D.; Garnero, P. Biochem. J. 2000, 345, 481.
4. Verzijil, N.; Degroot, J.; Thorpe, S. R.; Bank, R. A.; Shaw, J. N.; Lyons, T. J.; Bijlsma, J. W. J.; Lafeber, F. P. J. G.; Bayness, J. W.; Tekoppele, J. M. J. Biol. Chem. 2000, 275, 39027.
5. Cloos, P. A. C.; Fledelius, C. Biochem. J. 2000, 345, 473.
6. Bada, J. L.; Schroeder, R. A.; Protsch, R.; Berger, R. Proc. Natl. Acad. Sci. U.S.A. 1974, 71, 914.
7. Friedman, M.; Levin, C. E.; Noma, A. T. J. Food Sci. 1984, 49, 1282.
8. Friedman, M. J. Agric. Food Chem. 1999, 47, 3457.
9. Friedman, M. J. Agric. Food Chem. 1999, 47, 1295.
10. Axelsson, S. Med. Hypotheses 1998, 51, 47.
11. Bada, J. L.; Kvenvolden, K. A.; Peterson, E. Nature 1973, 245, 308.
12. Ramachandran, G. N.; Mitra, A. K. J. Mol. Biol. 1976, 107, 85.
13. Lutolf, M. P.; Hubbell, J. A. Nat. Biotechnol. 2005, 23, 47.
14. Beck, K.; Chan, V. C.; Shenoy, N.; Kirkpatrick, A.; Ramshaw, J. A. M.; Brodsky, B. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 4273.
15. Wang, A. Y.; Foss, C. A.; Leong, S.; Mo, X.; Pomper, M. G.; Yu, M. S. Biomacromolecules 2008, 9, 1755.
16. Lee, C. H.; Singla, A.; Lee, Y. Int. J. Pharm. 2001, 221, 1.
17. Yannas, I. V. Angew. Chem., Int. Ed. 1990, 29, 20.
18. Reddi, A. H. Tissue Eng. 2000, 6, 351.
19. Huynh, T.; Abraham, G.; Murray, J.; Brockbank, K.; Hagen, P. O.; Sullivan, S. Nat. Biotechnol. 1999, 17, 1083.
20. Thakar, R. G.; Ho, F.; Huang, N. F.; Liepmann, D.; Li, S. Biochem. Biophys. Res. Commun. 2003, 307, 883.
21. Koster, S.; Evans, H. M.; Wong, J. Y.; Pfohl, T. Biomacromolecules 2008, 9, 199.
22. Elsaid, K. A.; Chichester, C. O. Clin. Chim. Acta 2006, 365, 68.
23. Engel, J.; Bachinger, H. J. Top. Curr. Chem. 2005, 247, 7.
24. Treatise on Collagen; Ramachandran, G. N., Ed.; Academic Press: New York, 1964.
25. Rich, A.; Crick, F. H. J. Mol. Biol. 1961, 3, 483.
26. Bella, J.; Eaton, M.; Brodsky, B.; Berman, H. M. Science 1994, 266, 75.
27. Raman, S. S.; Parthasarathi, R.; Subramanian, V.; Ramasami, T. J. Phys. Chem. B 2006, 110, 20678.
28. Bella, J.; Eaton, M.; Brodsky, B.; Berman, H. M. Structure 1995, 3, 893.
29. Salem, G.; Traub, W. FEBS Lett 1975, 51, 94.
30. Dai, N.; Wang, X. J.; Etzkorn, F. A. J. Am. Chem. Soc. 2008, 130, 5396.
31. Perisikov, A. V.; Ramshaw, J. A. M.; Kirkpatrick, A.; Brodsky, B. Biochemistry 2000, 39, 14960.
32. Chan, V. C.; Ramshaw, J. A. M.; Kirkpatrick, A.; Beek, K.; Brodsky, B. J. Biol. Chem. 1997, 272, 31441.
33. Horng, J.; Kotch, F. W.; Raines, R. T. Protein Sci. 2007, 16, 208.
34. Tsai, M.; Xu, Y.; Dannenberg, J. J. J. Am. Chem. Soc. 2005, 127, 14130.
35. Shah, N. K.; Brodsky, B.; Kirkpartrick, A.; Ramshaw, J. A. M. Biopolymers 1999, 49, 297.
36. Krause, E.; Bienert, M.; Schmieder, P.; Wenschuh, H. J. Am. Chem. Soc. 2000, 122, 4865.
37. Aravinda, S.; Sharmala, N.; Desiraju, S.; Balaram, P. Chem. Commun. 2002, 20, 2454.
38. Venkatraman, J.; Shankaramma, S. C.; Balaram, P. Chem. Rev. 2001, 101, 3131.
39. Aravinda, S.; Sharmala, N.; Roy, R.; Balaram, P. Proc.-Indian Acad. Sci., Chem. Sci. 2003, 115, 373.
40. Anil, B.; Song, B.; Tang, Y.; Raleigh, D. P. J. Am. Chem. Soc. 2004, 126, 13194.
41. Anil, B.; Craig-Schapiro, R.; Raleigh, D. P. J. Am. Chem Soc. 2006, 128, 3144.
42. Fairman, R.; Anthony-CaChill, S. J.; DeGrado, W. F. J. Am. Chem. Soc. 1992, 114, 5458.
43. Mitchell, J. B. O.; Smith, J. Proteins 2003, 50, 563.
44. Valiyaveetil, F. I.; Sekedat, M.; MacKinnon, R.; Muir, T. W. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17045.
45. Xie, C.; Prahl, A.; Ericken, B.; Wu, Z.; Zeng, P.; Li, X.; Lu, W. Y.; Lubkowski, J.; Lu, W. J. Biol. Chem. 2005, 280, 32921.
46. Imperiali, B.; Moats, R. A.; Fisher, S. L.; Prins, T. J. J. Am. Chem. Soc. 1992, 114, 3182.
47. Struthers, M. D.; Cheng, R. P.; Imperiali, B. J. Am. Chem. Soc. 1996, 118, 3073.
48. Liardon, R.; Friedman, M. J. Agric. Food Chem. 1987, 35, 661.
49. Fischer, P. M. Curr. Protein Pept Sci. 2003, 4, 339.
50. Frau, J.; Price, S. L. J. Comput. -AidedMol. Des. 1996, 10, 107.
51. Pohl, E.; Sheldrick, G. M.; Fisher, S.; Lackner, H. Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 1994, 50, 100.
52. Marrifield, R. B.; Juvvadi, P.; Andreu, D.; Ubach, J.; Boman, A.; Boman, H. G. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 3449.
53. Wade, D.; Boman, A.; Wahlin, B.; Drain, C. M.; Andreu, D.; Boman, H. G.; Marrifield, R. B. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 4761.
54. Gayatri, R.; Sharma, A. K.; Rajaram, R.; Ramasami, T. Biochem. Biophys. Res. Commun. 2001, 283, 229.
55. Usha, R.; Raman, S. S.; Subramanian, V.; Ramasami, T. Chem. Phys. Lett 2006, 430, 391.
56. Gayatri, R.; Rajaram, R.; Ramasami, T. Biochim. Biophys. Acta 2000, 1524, 228.
57. Gustavson, K. H. The Chemistry of Tanning Process; Academic Press, Inc.: New York, 1956.
58. Raman, S. S.; Parthasarathi, R.; Subramanian, V.; Ramasami, T. J. Phys.Chem. B 2008, 112, 1533.
59. Raman, S. S.; Vijayaraj, R.; Parthasarathi, R.; Subramanian, V.; Ramasami, T. J. Mol. Struct. (THEOCHEM) 2008, 851, 299.
60. Shah, N. K.; Ramshaw, J. A. M.; Kirkpatrick, A.; Shah, C.; Brodsky, B. Biochemistry 1996, 35, 10262.
61. Shah, N. K.; Sharma, M.; Kirkpatrick, A.; Ramshaw, J. A. M.; Brodsky, B. Biochemistry 1997, 36, 5878.
62. Fields, G. B.; Prockop, D. J. Biopolymers 1996, 40, 345.
63. Stultz, C. M. Protein Sci. 2006, 15, 2166.
64. Bachinger, H. P.; Bruckner, P.; Timpl, R.; Prockop, D. J.; Engel, J. Eur. J. Biochem. 1980, 106, 619.
65. Babu, I. R.; Ganesh, K. N. J. Am. Chem. Soc. 2001, 123, 2079.
66. Sacca, B.; Renner, C.; Moroder, L. J. Mol. Biol. 2002, 324, 309.
67. Kwak, A.; Capua, A. D.; Locardi, E.; Goodman, M. J. Am. Chem. Soc. 2002, 124, 14085.
68. Long, C. G.; Bras well, E.; Zhu, D.; Apigo, J.; Baum, J.; Broadsky, B. Biochemistry 1993, 32, 11688.
69. Huang, C. C.; Couch, G. S.; Pettersen, E. F.; Ferrin, T. E.; Howard, A. E. Pac Symp. Biocomput. 1998, 349.
70. Klein, T. E.; Huang, C. C. Biopolymers 1999, 49, 167.
71. Pearlman, D. A.; Case, D. A.; Caldwell, J. C.; Seibel, G. L.; Singh, U. C.; Weiner, P.; Kollman, P. A. Comput. Phys. Commun. 1995, 91, 1.
72. Hornak, K. V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712.
73. Park, S.; Radmer, R.; Klevin, T.; Pande, V. S. J. Comput. Chem. 2005, 26, 1612.
74. Mongan, J. J. Comput. - Aided Mol. Des. 2004, 18, 433.
75. Westhof, E.; Sundaralingam, M. J. Am. Chem. Soc. 1983, 105, 970.
76. Shao, J.; Tanner, S. W.; Thompson, N.; Cheatham, T. E. J. Chem. Theory Comput. 2007, 3, 2312.
77. Brodsky, B.; Persikov, A. V. Adv. Protein Chem. 2005, 70, 301.
78. Persikov, A. V.; Brodsky, B. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1101.
79. Buevich, A. V.; Silva, T.; Brodsky, B.; Baum, J. J. Biol. Chem. 2004, 279, 46890.
80. Buevich, A. V.; Dai, Q. H.; Liu, X.; Brodsky, B.; Baum, J. Biochemistry 2000, 39, 4299.
81. Bella, J.; Eaton, M.; Brodsky, B.; Berman, H. M. Science 1994, 266, 75.
82. (a) Parthasarathi, R.; Subramanian, V. Hydrogen Bonding: New Insights; Challenges and Advances in Computational Chemistry and Physics 3; Grabowski, S. J., Ed.; Kluwer: New York, 2006.
83. (b) Parthasarathi, R.; Amutha, R.; Subramanian, V.; Nair, B. U.; Ramasami, T. J. Phys. Chem. A 2004, 108, 3817.
84. (c) Parthasarathi, R.; Raman, S. S.; Subramanian, V.; Ramasami, T. J. Phys. Chem. A 2007, 111, 7141.
85. Beck, J.; Chan, V. C.; Shenoy, N.; Kirkpatrick, A.; Ramshaw, J. A. M.; Brodsky, B. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 4273.